Terminate nextflow on errors

iqbal-lab-org · Mar 6, 2018 · 412d6cc · 412d6cc
1 parent 395ba37
commit 412d6cc
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/minos/multi_sample_pipeline.py b/minos/multi_sample_pipeline.py
@@ -176,7 +176,7 @@ def _write_nextflow_script(cls, outfile):
 
 
 process cluster_small_vars_vcf {
-    errorStrategy {task.attempt < 3 ? 'retry' : 'ignore'}
+    errorStrategy {task.attempt < 3 ? 'retry' : 'terminate'}
     memory {params.testing ? '0.5 GB' : 1.GB * params.cluster_small_vars_ram * task.attempt}
     maxRetries 3
 
@@ -197,7 +197,7 @@ def _write_nextflow_script(cls, outfile):
 
 
 process gramtools_build_small_vars {
-    errorStrategy {task.attempt < 3 ? 'retry' : 'ignore'}
+    errorStrategy {task.attempt < 3 ? 'retry' : 'terminate'}
     memory {params.testing ? '0.5 GB' : 1.GB * params.gramtools_build_small_vars_ram * task.attempt}
     maxRetries 3
 
@@ -227,7 +227,7 @@ def _write_nextflow_script(cls, outfile):
 
 
 process minos_all_small_vars {
-    errorStrategy {task.attempt < 3 ? 'retry' : 'ignore'}
+    errorStrategy {task.attempt < 3 ? 'retry' : 'terminate'}
     memory {params.testing ? '0.5 GB' : 1.GB * params.minos_small_vars_ram * task.attempt}
     maxRetries 3
 
@@ -281,7 +281,7 @@ def _write_nextflow_script(cls, outfile):
 
 
 process bcftools_merge {
-    errorStrategy {task.attempt < 3 ? 'retry' : 'ignore'}
+    errorStrategy {task.attempt < 3 ? 'retry' : 'terminate'}
     memory {params.testing ? '0.5 GB' : 1.GB * params.bcftools_merge_ram * task.attempt}
     maxRetries 3
 

diff --git a/setup.py b/setup.py
@@ -4,7 +4,7 @@
 
 setup(
     name='bio-minos',
-    version='0.2.0',
+    version='0.3.0',
     description='Variant call adjudication',
     packages = find_packages(),
     author='Martin Hunt',